1. Field of the Invention
The present invention relates to novel compositions and sequences useful for the evaluation of T cell receptor genes and their expression, and therapeutic applications thereof.
2. Description of the Background
T cells constitute a cellular component of the immune system that is able to identify and target foreign antigens for destruction by the immune system. At the same time, T cells must be able to identify cells from the host organism, so that the immune system does not attack the body itself. T cells interact with antigens and the body through receptors (T cell receptors; TCR) located on the T cell surface.
TCRs are heterodimers having an alpha (α) and a beta (β) subunit, each of which include variable (V) and constant (C) regions. It is the variable region of these chains that directly contacts the major histocompatibility (a:MHC) complex located on the surface of all cells, thereby eliciting the T cell response. Each individual has multiple TCRV(α) and TCRV(β) gene segments, providing for the ability to respond to a large number of a:MHCs.
Prior to 1995, there was no uniform or systematic organization of the genetic sequences that code for the TCRVα and TCRVβ families. An international group was created to address this problem, and, as a result, Arden, Clark, Kabelitz, and Mak (Immunogenetics 42, 455; 1995, which is hereby incorporated by reference) applied a consistent classification scheme to all known human TCRVα and TCRVβ gene families. Based on this classification system, there are 32 different functional variable α families with 69 subfamily members and 25 different functional variable β families with 91 subfamily members. According to the proposed nomenclature, TCRs are named according to the following convention, receptor subunit; family; subfamily; allele. Thus, AV1S2A3 refers to the T cell receptor α variable receptor, family 1, subfamily 2, and allele 3. This naming convention will be used herein.
It is of great clinical and scientific interest to evaluate the expression of TCR families accurately in individual patients, as this repertoire is a reflection of the immune response in those patients. One possible way to analyze the expression of T cell receptors could be through the use of antibody-based analysis of the surface receptor protein. However, a comprehensive evaluation is not currently possible due to the lack of antibodies to all of the different members of human TCR variable α and β families.
An alternative approach is to analyze gene expression of the TCRVα and TCRVβ regions. Previous attempts at establishing methods to evaluate the expression of all members of the TCR families have not taken into account the new systematic classification of Arden et al. or the wide variety of subfamilies and alleles that exist for many of the variable families. Accordingly, nucleotide probes that have been previously published in the literature do not consistently recognize all subfamily members of a particular TCR family. For example, a nucleotide probe may only recognize the AV2S1A1 and not the other alleles and subfamily members of the AV2 family. Therefore, no broad statements regarding the expression of the AV2 family may be made using this probe. Given the large degree of diversity among TCRs, the inadequacy of presently-available nucleotide probes dramatically reduces their clinical and experimental utility.
Thus, there has been a long-standing need in the molecular biological and clinical communities for a genetic tool that can be used to evaluate specifically the expression of the T cell surface receptors in a patient. The genetic tool should be able to identify each family of α and β TCRs independently, while, at the same time, recognizing all subfamily members and alleles within that family. Such a collection of nucleotide probes would significantly advance the state of the art and the ability of clinicians to evaluate the repertoire of T cells in the body.